Relative impact of seasonal and oceanographic drivers on surface chlorophyll a along a Western Boundary Current

Strengthening Western Boundary Currents (WBCs) advect warm, low nutrient waters into temperate latitudes, displacing more productive waters. WBCs also influence phytoplankton distribution and growth through current-induced upwelling, mesoscale eddy intrusion and seasonal changes in strength and poleward penetration. Here we examine dynamics of chlorophyll a (Chl. a) in the western Pacific Ocean, a region strongly influenced by the East Australian Current (EAC). We interpreted a spatial and temporal analysis of satellite-derived surface Chl. a, using a hydrodynamic model, a wind-reanalysis product and an altimetry-derived eddy-census. Our analysis revealed regions of persistently elevated surface Chl. a along the continental shelf and showed that different processes have a dominant effect in different locations. In the northern and central zones, upwelling events tend to regulate surface Chl. a patterns, with peaks in phytoplankton biomass corresponding to two known upwelling locations south of Cape Byron (28.5°S) and Smoky Cape (31°S). Within the central EAC separation zone, positive surface Chl. a anomalies occurred 65% of the time when both wind-stress (τw) and bottom-stress (τB) were upwelling-favourable, and only 17% of the time when both were downwelling-favourable. The interaction of wind and the EAC was a critical driver of surface Chl. a dynamics, with upwelling-favourable τW resulting in a 70% increase in surface Chl. a at some locations, when compared to downwelling-favourable τW. In the southern zone, surface Chl. a was driven by a strong seasonal cycle, with phytoplankton biomass increasing up to 152% annually each spring. The Stockton Bight region (32.25-33.25°S) contained ≥20% of the total shelf Chl. a on 27% of occasions due to its location downstream of upwelling locations, wide shelf area and reduced surface velocities. This region is analogous to productive fisheries regions in the Aghulus Current (Natal Bight) and Kuroshio Current (Enshu-nada Sea). These patterns of phytoplankton biomass show contrasting temporal dynamics north and south of the central EAC separation zone with more episodic upwelling-driven Chl. a anomalies to the north, compared with regular annual spring bloom dynamics to the south. We expect changes in the strength of the EAC to have greater influence on shelf phytoplankton dynamics to the north of the separation zone. © 2013 Elsevier Ltd

Three-dimensional structure of a swarm of the salp Thalia democratica within a cold-core eddy off southeast Australia

Swarms of the salp Thalia democratica periodically occur off southeast Australia following the austral spring bloom of phytoplankton. In October 2008 a filament of upwelled water was advected south by the adjacent East Australian Current and formed a 30km diameter cold-core eddy (CCE). The three-dimensional structure of a subsurface swarm of T. democratica within the eddy was examined using both oblique and vertical hauls and an optical plankton counter (OPC) deployed on a towed body. The CCE displayed distinct uplift of the nutricline and elevated fluorescence. Net samples show the zooplankton community was dominated by T. democratica, comprising 73%-88% of zooplankton abundance. The size distribution of T. democratica measured from net samples was 0.5-5mm and was used to interpret the OPC transects, which showed the swarm formed a 15km diameter disc located 20-40m deep in the center of the eddy. The maximum salp abundance was in the pycnocline and coincided with the subsurface fluorescence maximum. The mean abundance of T. democratica size particles within the disc was 5003 individuals m-3 (ind. m-3), contrasted with only 604 ind. m-3 at the outer edge of the eddy. The vertically concentrated and horizontally constrained disc-shaped salp swarm occurred at the interface of salp-bearing inner shelf water and nutrient-rich upwelled water in a CCE. The physical processes that formed the CCE on the inshore edge of the western boundary current led to the largest density of salps recorded. Copyright 2011 by the American Geophysical Union

Planet Populations as a Function of Stellar Properties

Exoplanets around different types of stars provide a window into the diverse environments in which planets form. This chapter describes the observed relations between exoplanet populations and stellar properties and how they connect to planet formation in protoplanetary disks. Giant planets occur more frequently around more metal-rich and more massive stars. These findings support the core accretion theory of planet formation, in which the cores of giant planets form more rapidly in more metal-rich and more massive protoplanetary disks. Smaller planets, those with sizes roughly between Earth and Neptune, exhibit different scaling relations with stellar properties. These planets are found around stars with a wide range of metallicities and occur more frequently around lower mass stars. This indicates that planet formation takes place in a wide range of environments, yet it is not clear why planets form more efficiently around low mass stars. Going forward, exoplanet surveys targeting M dwarfs will characterize the exoplanet population around the lowest mass stars. In combination with ongoing stellar characterization, this will help us understand the formation of planets in a large range of environments.Comment: Accepted for Publication in the Handbook of Exoplanet

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Vertically Resolved Pelagic Particle Biomass and Size Structure Across a Continental Shelf Under the Influence of a Western Boundary Current

Continental shelves are key to societal interactions with the oceans, supporting >90% of the world's fisheries through highly productive ecosystems. Previous research has shown that phytoplankton biomass is generally higher on the inner continental shelves, often due to increased nutrient inputs from upwelling or coastal run-off. However, consistency in observed vertical and horizontal gradients (in abundance, biomass or size) of larger particulates, including zooplankton, on continental shelves has not been established. Using an optical plankton counter and CTD mounted on an undulating towed body, we present high-resolution vertically resolved profiles of pelagic particle size structure across a continental shelf. Biomass was highest inshore, declining with distance from shore and with depth in the top 100 m of the water column, although the presence of frontal zones can alter this pattern. In the region adjacent to the East Australian Current (EAC), uplift generated by either the EAC interacting with the continental slope or upwelling-favorable winds, correlated with smaller geometric mean sizes and steeper size spectrum slopes, particularly in the presence of frontal features. South of the EAC separation, the continental shelf water mass was more homogenous but still displayed the same horizontal and vertical patterns in particulate biomass and mean size. By combining our observations in a global comparison, we demonstrate consistent particulate distributions on continental shelves where the inner shelf has higher biomass with a steeper size spectrum slope compared to offshore. The highly productive inner shelf supports zooplankton communities vital to temperate ecosystems and coastal fisheries, through their consistently high biomass

Unravelling the genome-wide contributions of specific 2-alkyl-4-quinolones and PqsE to quorum sensing in Pseudomonas aeruginosa

The pqs quorum sensing (QS) system is crucial for Pseudomonas aeruginosa virulence both in vitro and in animal models of infection and is considered an ideal target for the development of anti-virulence agents. However, the precise role played by each individual component of this complex QS circuit in the control of virulence remains to be elucidated. Key components of the pqs QS system are 2-heptyl-4-hydroxyquinoline (HHQ), 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline N-oxide (HQNO), the transcriptional regulator PqsR and the PQS-effector element PqsE. To define the individual contribution of each of these components to QS-mediated regulation, transcriptomic analyses were performed and validated on engineered P. aeruginosa strains in which the biosynthesis of 2-alkyl 4-quinolones (AQs) and expression of pqsE and pqsR have been uncoupled, facilitating the identification of the genes controlled by individual pqs system components. The results obtained demonstrate that i) the PQS biosynthetic precursor HHQ triggers a PqsR-dependent positive feedback loop that leads to the increased expression of only the pqsABCDE operon, ii) PqsE is involved in the regulation of diverse genes coding for key virulence determinants and biofilm development, iii) PQS promotes AQ biosynthesis, the expression of genes involved in the iron-starvation response and virulence factor production via PqsR-dependent and PqsR-independent pathways, and iv) HQNO does not influence transcription and hence does not function as a QS signal molecule. Overall this work has facilitated identification of the specific regulons controlled by individual pqs system components and uncovered the ability of PQS to contribute to gene regulation independent of both its ability to activate PqsR and to induce the iron-starvation response

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

The effect of surface flooding on the physical-biogeochemical dynamics of a warm-core eddy off southeast Australia

Warm-core eddies (WCEs) formed from the East Australian Current (EAC) play an important role in the heat, mass and biogeochemical budgets of the western Tasman Sea. The development and separation of an EAC WCE during July-December 2008 was observed using remotely sensed temperature, ocean colour and sea-level elevation, three Argo floats, a shipboard CTD, a shelf mooring array and a 15-day deployment of a Slocum glider. The eddy formed from an EAC meander during the first half of 2008 and in late August had a ~275m deep surface mixed layer. In the two months before separation in early December, fresher and warmer EAC water flooded the top of the eddy, submerging the winter mixed layer. The rate of vertical transport due to submergence was estimated to be between 1 and 6Sv, at the time accounting for a significant fraction of the mean southward flow of the EAC. The core of the eddy had a surface chlorophyll a concentration of <0.4mgm-3 throughout the observations. A 20-40m thick pycnocline formed at the interface of the flooding surface waters and the submerged layer. Chlorophyll a concentration in the pycnocline ranged from 0.5 to 2mgm-3, with depth-integrated concentration ranging between 25 and 75mgm-2. The development of a sub-surface maximum suggests that flooding increased light levels in the pycnocline. Elevated levels of coloured dissolved organic matter in the submerged layer correspond to oxygen depletion, suggesting respiration of organic matter. A comparison is made with observations from WCEs in 1978 and 1997 in which, unusually, surface flooding did not occur, but solar heating stratified the top 50m. In the two eddies with surface capping, surface chlorophyll a concentrations were an order of magnitude higher than the 2008 flooded eddy, but depth-integrated chlorophyll a was similar. These findings suggest that EAC WCEs with relatively shallow surface flooding contain more phytoplankton biomass than surface images would suggest, with the vertical position of the chlorophyll a maximum depending on whether, and to what depth, the winter surface mixed layer is submerged. © 2010 Elsevier Ltd

An integrated ontology resource to explore and study host-virus relationships.

Our growing knowledge of viruses reveals how these pathogens manage to evade innate host defenses. A global scheme emerges in which many viruses usurp key cellular defense mechanisms and often inhibit the same components of antiviral signaling. To accurately describe these processes, we have generated a comprehensive dictionary for eukaryotic host-virus interactions. This controlled vocabulary has been detailed in 57 ViralZone resource web pages which contain a global description of all molecular processes. In order to annotate viral gene products with this vocabulary, an ontology has been built in a hierarchy of UniProt Knowledgebase (UniProtKB) keyword terms and corresponding Gene Ontology (GO) terms have been developed in parallel. The results are 65 UniProtKB keywords related to 57 GO terms, which have been used in 14,390 manual annotations; 908,723 automatic annotations and propagated to an estimation of 922,941 GO annotations. ViralZone pages, UniProtKB keywords and GO terms provide complementary tools to users, and the three resources have been linked to each other through host-virus vocabulary